Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, Ukraine

Authors: SAPKOTA, MANOJ - Cornell University; ZHAO, DONGYAN - Cornell University; BEIL, CRAIG - Cornell University; SHEEHAN, MOIRA - Cornell University; GREENE, STEPHANIE - Retired ARS Employee; Irish, Brian

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 12/24/2023
Publication Date: 1/12/2024
Citation: Sapkota, M., Zhao, D., Beil, C., Sheehan, M., Greene, S., Irish, B.M. 2024. Genetic diversity, population structure, and taxonomic confirmation in annual medic (Medicago spp.) collections from Crimea, Ukraine. Plant and Animal Genome Conference. PAG32.

Interpretive Summary:

Technical Abstract: An annual medic (Medicago spp.) germplasm collection was assembled from the Crimean Peninsula of Ukraine in 2008 to fill gaps in geographic coverage in the USDA ARS National Plant Germplasm System (NPGS) temperate-adapted forage legume collections. A total of 102 accessions across 10 Medicago species were collected. To assess genetic diversity, population structure, and to confirm taxonomic identities, the collections were phenotypically and genetically characterized. The phenotypic assessment encompassed 25 descriptor traits while genetic characterization was conducted using a 3K Diversity Array Technologies (DArTag) panel originally developed for alfalfa (Medicago sativa L.). For both field and molecular characterizations, a reference set of 92 geographically diverse and species-representative accessions were obtained from the NPGS collection. Phenotypic descriptors showed consistency among replicated plants within accessions, some variation across accessions within species, and evident distinctions between species. Because the DArTag panel was developed for cultivated alfalfa, the transferability of markers to the species being evaluated was partial, resulting in the detection of an average of ~1,500 marker loci per species. A total of 448 markers were present in 95% of the samples, likely representing conserved regions in all examined species. Exploring the occurrence of the missing markers revealed a significant difference among the species (p-value: 1.13e-47). Notably, a general trend emerged where, as genetic distance from M. sativa increased, the number of missing marker loci also tended to rise. Principal component and phylogenetic analyses based on markers (n = 2,396) present in >5% of the samples demonstrated accessions clustered by species and predicted evolutionary relationships consistent with the observed genetic distance among the species. Our analyses also revealed the presence of unique genetic diversity in accessions for certain species from the Crimean collection based on distinct clustering patterns and genetic signatures. Additionally, the markers aided in the taxonomic identity of a few accessions that were likely mislabeled. The genotyping results also showed that sampling individual plants for these mostly self-pollinating species is sufficient due to high reproducibility between three single and one pooled (n=7) biological replicate leaf samples. In conclusion, the phenotyping and the 2,396 SNP marker set were useful in estimating population structure highlighting novel and unique genetic diversity captured in the Crimean accessions. While prior research has touched upon these aspects, the comprehensive inclusion of all these species in a single study is unique, consequently filling a previously existing knowledge gap. Furthermore, this research showed that the alfalfa 3K DArTag panel could be used in a similar fashion to evaluate other plant genetic resource collections of related Medicago.